scimap/spatiallda (nf-core#5260)

* Add phenotyped data under imaging/downstream

* Add the scimap implementation of spatialLDA

* passes lint and tests

* now it has real tests

* Added stub tests

* Prettifies

* exclude scimap/spatiallda from executing conda test

* This works! :D

.github/workflows/test.yml

@@ -565,6 +565,8 @@ jobs:
             tags: molkartgarage/clahe
           - profile: conda
             tags: quartonotebook
+          - profile: conda
+            tags: scimap/spatiallda
           - profile: conda
             tags: sentieon/bwaindex
           - profile: conda

modules/nf-core/scimap/spatiallda/main.nf

@@ -0,0 +1,50 @@
+process SCIMAP_SPATIALLDA {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "docker.io/miguelib/scimap:0.0.3"
+
+    input:
+    tuple val(meta), path(phenotyped)
+
+    output:
+    tuple val(meta), path("*.csv") , emit: spatial_lda_output
+    tuple val(meta), path("*.png") , emit: composition_plot
+    tuple val(meta), path("*.html"), emit: motif_location_plot
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    python /scimap/scripts/spatialLDA.py \
+        --input $phenotyped \
+        --output "${prefix}.csv" \
+        --neighborhood-composition-plot "${prefix}.png" \
+        --motif-locations-plot "${prefix}.html" \
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scimap/spatialLDA: \$(python /scimap/scripts/spatialLDA.py --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch "${prefix}.csv"
+    touch "${prefix}.png"
+    touch "${prefix}.html"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scimap/spatialLDA: \$(python /scimap/scripts/spatialLDA.py --version)
+    END_VERSIONS
+    """
+}

modules/nf-core/scimap/spatiallda/meta.yml

@@ -0,0 +1,52 @@
+name: "scimap_spatiallda"
+description: SpatialLDA uses an LDA based approach for the identification of cellular neighborhoods, using cell type identities.
+keywords:
+  - spatial_neighborhoods
+  - scimap
+  - spatial_omics
+tools:
+  - "scimap":
+      description: "Scimap is a scalable toolkit for analyzing spatial molecular data. The underlying framework is generalizable to spatial datasets mapped to XY coordinates. The package uses the anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. The Python-based implementation efficiently deals with large datasets of millions of cells."
+      homepage: "https://scimap.xyz/"
+      documentation: "https://scimap.xyz/tutorials/1-scimap-tutorial-getting-started/"
+      tool_dev_url: "https://github.com/labsyspharm/scimap"
+      doi: "10.5281/zenodo.7854095"
+      licence: ["MIT licence"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - phenotyped:
+      type: file
+      description: Phenotyped CSV file, it must contain the columns, sampleID, X, Y and Phenotype.
+      pattern: "*.{csv}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - spatial_lda_output:
+      type: file
+      description: File with the motifs detected from SpatialLDA
+      pattern: "*.{csv}"
+  - composition_plot:
+      type: file
+      description: Plot with the motif composition and the cell type composition of motifs.
+      pattern: "*.{png}"
+  - motif_location_plot:
+      type: file
+      description: Plot with the locations of the motifs.
+      pattern: "*.{html}"
+authors:
+  - "@migueLib"
+  - "@chiarasch"
+maintainers:
+  - "@migueLib"
+  - "@chiarasch"

modules/nf-core/scimap/spatiallda/tests/main.nf.test

@@ -0,0 +1,55 @@
+nextflow_process {
+
+    name "Test Process SCIMAP_SPATIALLDA"
+    script "../main.nf"
+    config "./nextflow.config"
+    process "SCIMAP_SPATIALLDA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "scimap"
+    tag "scimap/spatiallda"
+
+    test("spatiallda - csv") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.test_data['imaging']['downstream']['phenotyped'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.spatial_lda_output },
+                { assert process.out.composition_plot },
+                { assert process.out.motif_location_plot },
+                { assert process.out.versions },
+                { assert snapshot(process.out.versions).match("versions") },
+            )
+        }
+    }
+    test("spatiallda - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.test_data['imaging']['downstream']['phenotyped'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+    }
+}

modules/nf-core/scimap/spatiallda/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: "SCIMAP_SPATIALLDA" {
+        ext.args = '--phenotype phenotype --x-coordinate X_centroid --y-coordinate Y_centroid --sample-id sampleid --radius 30 --num-motifs 10 --method radius'
+    }
+}

modules/nf-core/scimap/spatiallda/tests/tags.yml

@@ -0,0 +1,2 @@
+scimap/spatiallda:
+  - "modules/nf-core/scimap/spatiallda/**"

tests/config/test_data.config

@@ -793,6 +793,7 @@ params {
             'downstream' {
                 markers                 = "${params.test_data_base}/data/imaging/downstream/markers.csv"
                 cell_feature_array      = "${params.test_data_base}/data/imaging/downstream/cycif_tonsil_cell.csv"
+                phenotyped              = "${params.test_data_base}/data/imaging/downstream/phenotyped.csv"
             }
             'background_subtraction' {
                 markers                 = "${params.test_data_base}/data/imaging/background_subtraction/markers.csv"